Hi,
I just noticed a problem with FEAT output images - post stats images
appear to have no activation, due to a LUT error. All above-threshold
voxels appear white instead of having the appropriate heat map applied.
I believe this is due to a change/bug in slicer:
slicer rendered_thresh_zstat1.nii.gz -d -S 2 750 rendered_thresh_zstat1.png
Option 0: -d
Option 1: -S 2 750 rendered_thresh_zstat1.png
-S 2 750 rendered_thresh_zstat1.png
Entries in LUT: 0
Intensity min, max : -4.03287 3.23551
Doesn't find any LUT. Some of my rendered* files appear to have
render1t specified in their header's aux_file while others do not
(version dependent??) but this does not seem to help slicer find the
correct LUT. Manually specifying -l render1t correctly loads the LUT
but does not scale it properly - intensity min, max are set to the
[0.02, .98] percentile range instead of the header cal_min, cal_max.
Changing featlib.tcl as follows:
fsl:exec "$FSLDIR/bin/overlay $fmri(rendertype) 0 $underlying -a
thresh_$rawstats $fmri(zmin) $fmri(zmax) rendered_thresh_$rawstats"
# Had to modify this - SG
#fsl:exec "${FSLDIR}/bin/slicer rendered_thresh_$rawstats $SLICER 750 rendered_thresh_${rawstats}.png"
set iminmax [ fsl:exec "${FSLDIR}/bin/fslstats rendered_thresh_$rawstats -R 2>/dev/null" ]
set imin [ lindex $iminmax 0 ]
set imax [ lindex $iminmax 1 ]
fsl:exec "${FSLDIR}/bin/slicer rendered_thresh_$rawstats -l render1t -i $imin $imax $SLICER 750 rendered_thresh_${rawstats}.png"
Appears to fix the problem. I am running 4.1.5 from the
neuro.debian.net repository on Ubuntu 9.10, tried in both 32 and 64 bit
machines (i have also tried directly compiling those sources, and that
does not help). I am not positive when the above broke as I upgrade
frequently and do not always look at FEAT output (as I usually do
further analysis or view on the surface via Freesurfer), but slicer has
rendered correctly on my machines in the past
Thanks,
-Scott Gorlin
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